That is fine for simple projects where all you have to do is automate cert updates for the root domain or a few subdomains. The problem is not to automate this process. It's easy to write a shellscript that regularly updates certs for a root domain or some subdomains.

The problem is that letsencrypt does not offer url based authentification for wildcard certs.

So you have to temper with your DNS infrastructure so that you can automate DNS updates for your domain.